[BioSQL-l] bioseqDB error

[Hilmar Lapp]

Hi -

you will only need to install Bioperl-db if you intend to use BioPerl  
to retrieve and store objects from/to the database. Also, Bioperl-db  
comes with scripts for loading sequences and ontologies (through  
BioPerl's SeqIO and OntologyIO capabilities).

load_ncbi_taxonomy.pl is independent of BioPerl or Bioperl-db (which  
is why I am pulling the thread back to BioSQL - problems with  
load_ncbi_taxonomy are unrelated to Bioperl).

If you see the error below only after 'installing' Bioperl-db I  
assume that you also ran the Bioperl-db test suite (as otherwise it  
is not explainable). Did this not result in any errors? The Bioperl- 
db tests normally clean up after themselves, and what you report  
seems to indicate that they are not. Are you using MySQL, and if so,  
did you make sure to enable InnoDB?

	-hilmar

On Jan 28, 2008, at 4:07 PM, snoze pa wrote:

> Still I am getting the same error message..
>
> My question is:
>
> Do i need to install bioperl-DB for biosql?
>
> When I am using biosql and trying to load NCBI taxonomy then it is  
> working
> fine. but when I am trying to install bioperl-DB then it is giving me
> following error message when loading NCBI taxonomy.
>
> Any help?
>
>
>
> Loading NCBI taxon database in taxdata:
>         ... retrieving all taxon nodes in the database
>         ... reading in taxon nodes from nodes.dmp
>         ... insert / update / delete taxon nodes
> failed to insert node (10090;10090;10088;species;1;2): Duplicate entry
> '10090' for key 2 at load_ncbi_taxonomy.pl line 568
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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